Modern Infectious Disease Epidemiology (eBook)

Foreword 5
Acknowledgements 8
Contents 9
Contributors 11
Part I Challenges 15
1 The Global Burden of Infectious Diseases 16
1.1 Introduction 16
1.2 The Burden of Disease Approach 17
1.2.1 Conceptual Framework 17
1.2.2 The Measurement Unit Disability-Adjusted Life Year (DALY) 18
1.3 The global and Regional Burden of Infectious Diseases 21
1.3.1 Infectious Diseases and the Global and Regional Causes of Death 21
1.3.2 Infectious Diseases and the Global and Regional Burden of Disease Burden of disease 25
1.3.3 Projections of the Global Burden of Infectious Diseases from 2002 to 2030 30
1.4 Discussion 32
References 33
2 Global Challenges of Infectious Disease Epidemiology 35
2.1 Introduction 35
2.2 Challenges 35
2.2.1 Demographic Transition and Aging 36
2.2.2 Mobility 37
2.2.3 Modern Medical Practices 39
2.2.4 Modern Food Technology 41
2.2.5 Politics and Environment 42
2.2.6 Urbanization and Megacities 43
2.3 Solution Strategies to Meet These Challenges 46
2.3.1 Functions of Infectious Disease Epidemiology 46
2.3.2 Interdisciplinary Approaches 47
References 48
3 Emerging and Re-emerging Infectious Diseases 51
3.1 Definition 51
3.2 Factors Contributing to Emergence 51
3.3 New Infectious Agents in Old Diseases 54
3.3.1 Emerging Diagnosis of Infectious Diseases 56
3.3.1.1 Helicobacter pylori-Associated Diseases 56
3.3.1.2 Lyme Disease, Tick-Borne Encephalitis 56
3.3.1.3 Norovirus 58
3.3.1.4 Hepatitis E 58
3.3.1.5 Cervix Carcinoma and Human Papillomavirus Infection 59
3.4 Newly Emerging Infections 59
3.4.1 New Variant of Creutzfeldt-Jakob Disease 61
3.4.2 Nipah Virus Encephalitis 61
3.4.3 West Nile Encephalitis 61
3.4.4 Severe Acute Respiratory Syndrome (SARS) 62
3.4.5 Hantavirus 62
3.4.6 Filoviruses and Lassa Virus 63
3.4.7 C. difficile Ribotype 027 64
3.5 Re-emerging Infectious Diseases 64
3.5.1 Cholera 66
3.6 Vector-Borne Diseases 67
3.6.1 Chikungunya Fever 67
3.6.2 Ross River Fever 67
3.6.3 Japanese Encephalitis (JE) 68
3.6.4 Crimean-Congo Hemorrhagic Fever (CCHF) 68
3.6.5 Rift Valley Fever (RVF) 68
3.6.6 Leishmaniasis 69
3.7 Emerging Resistance 69
3.8 Outlook 73
3.9 Summary 76
References 77
4 Infectious Disease Control Policies and the Role of Governmental and Intergovernmental Organisations 80
4.1 Introduction 80
4.2 The International Health Regulations 81
4.3 The World Health Organisation 86
4.4 The Centers for Disease Control and Prevention, USA 87
4.5 The European Centre for Disease Prevention and Control (ECDC) 88
4.6 Other International Players 90
4.7 Conclusion 91
References 92
Part II General Concepts and Methods 94
5 Principles of Infectious Disease Epidemiology 95
5.1 Definition and Aims of Epidemiology 95
5.2 Epidemiology and Public Health 96
5.2.1 Example: Epidemiology and the HIV/AIDS Epidemic 97
5.2.1.1 Elucidating the Aetiology 97
5.2.1.2 Describing the Spectrum of Disease for HIV/AIDS 98
5.2.1.3 Describing the Natural History of HIV Infection 98
5.2.1.4 Risk Factors and Protective Factors for HIV Infection 98
5.2.1.5 Predicting Disease Trends 98
5.2.1.6 To Estimate Disease Burdens and Health-Care Needs of a Population 99
5.2.1.7 To Test the Effectiveness of Interventions 99
5.3 Characteristics of Infectious Disease Epidemiology 99
5.3.1 Exposure 101
5.3.2 Infection 102
5.3.3 Stages of Infection and Disease 103
5.3.4 Virulence, Pathogenicity and Immunogenicity 105
5.3.5 Routes of Transmission 105
5.3.6 Endemic Infectious Diseases and Epidemic Outbreaks 107
5.4 Challenges of Infectious Disease Epidemiology 107
References 108
6 Social Risk Factors 110
6.1 Introduction 110
6.2 Pathways 111
6.3 Outcome Variables 112
6.4 Social Risk Factors 113
6.5 Routine Health Statistics 113
6.6 Classical Studies 115
6.7 Studies Centring Round a Single Dichotomous Risk Factor 117
6.8 Community Studies 118
6.9 Surveys on the Literature 120
6.10 Discussion 120
6.11 Implications for Public Health Policy 121
References 122
7 Molecular Typing and Clustering Analysis as a Tool for Epidemiology of Infectious Diseases 125
7.1 Introduction 125
7.2 Attributes for Successful Typing 127
7.3 Genotyping Methods 127
7.3.1 Plasmid Typing 127
7.3.2 RFLP, PFGE, and Ribotyping 128
7.3.3 PCR--RFLP 130
7.3.4 RAPD and AP-PCR 130
7.3.5 AFLP 131
7.3.6 MLVA 132
7.4 Hybridization Arrays 134
7.4.1 Spoligotyping 134
7.4.2 Microarrays 136
7.5 Sequence-Based Typing (SBT) Analysis 136
7.5.1 SLST 137
7.5.2 MLST 137
7.5.3 Whole Genome Sequencing 138
7.5.4 SNP Genotyping 138
7.6 Cluster Analysis 139
7.6.1 Cluster Analysis for Nosocomial and Community-Acquired Outbreaks 140
7.6.2 Cluster Analysis and Linkage to Risk Groups 141
7.6.2.1 Human Immunodeficiency Virus 141
7.6.2.2 Hepatitis A Virus 142
7.6.2.3 Neisseria gonorrhoeae 143
7.6.2.4 Methicillin-Resistant S. aureus 143
7.7 Limitations of Typing 144
7.8 Concluding Remarks 145
References 147
8 Epidemiologic Surveillance 150
8.1 Introduction 150
8.2 History 151
8.3 Sources of Information 152
8.4 Form and Content of Information 154
8.5 Mechanisms of Surveillance 155
8.6 Objectives of Surveillance 157
8.7 Some Examples of Specific Surveillance Systems 158
8.8 A Guide to Further Study 162
References 162
9 Outbreak Investigations 165
9.1 Introduction 165
9.2 Defining an Outbreak 166
9.3 Suspicions of an Outbreak and Risk Communication 167
9.4 Descriptive Analysis 168
9.4.1 Case Definition 169
9.4.2 Finding Cases and Collecting Information 170
9.4.3 Time: Epidemic Curves of Outbreaks 171
9.4.4 Place: Spatial distribution 172
9.4.5 Person: Portraying the Outbreak Population 173
9.5 Exhibit 9.1 Use of mathematical methods in outbreak investigation 173
9.5 Analytical Epidemiology 174
9.5.1 Formulating a Hypothesis 175
9.5.2 Assessing Risks: Historical Cohort Studies 175
9.5.2.1 Example of a Cohort Study in a Hypothetical Foodborne Outbreak 176
9.5.3 Secondary Attack Rate 177
9.5.4 Case--Control Study 178
9.5.4.1 Example of a Case--Control Study in a Hypothetical Foodborne Outbreak 178
9.5.5 Proving Evidence for Causal Associations 179
9.6 Control Measures and Reporting 179
9.7 Conclusions 180
References 181
10 Geographic Information Systems 183
10.1 Introduction 183
10.2 A Conceptual Framework for GI Science in the IDE Context 184
10.3 Principles of Geoinformation Processing 185
10.3.1 Data and Databases 185
10.3.2 Geovisualisation 187
10.3.3 Map Operations and Analytical Models in GIS 189
10.3.4 The Role of Remote Sensing 193
10.4 Conclusion and Future Perspectives 195
References 196
11 Methods and Concepts of Epidemiology 198
11.1 Introduction 198
11.2 Definitions of Epidemiological Terms 198
11.2.1 Measures of Disease Occurrence 198
11.2.2 Measures of Association 199
11.3 Populations, Study Samples and Random Error 201
11.4 Common Types of Epidemiological Studies 202
11.5 Ethic in Epidemiological Research 206
11.6 Causality in Epidemiological Research 207
11.7 Systematic Error in Epidemiological Studies 208
11.8 Methodological Issues of Diagnostic Tests 209
11.9 Outlook on the Use of Mathematical Modelling in Infectious Disease Epidemiology 210
References 211
12 Mathematical Models in Infectious Disease Epidemiology 214
12.1 Introduction 214
12.2 Basic Concepts in Mathematical Modeling 215
12.3 Basic Concepts: Reproduction Number, Final Size, Endemic Steady State, and Critical Vaccination Coverage 220
12.3.1 Advanced Models 222
12.3.1.1 More Complex Compartmental Models 222
12.3.1.2 Models with Continuous Age Structure 223
12.3.1.3 Stochastic Transmission Models 223
12.3.1.4 Network Models 224
12.4 Use of Modeling for Public Health Policy 224
12.5 Further Reading 225
References 225
13 Immunity to Infectious Diseases 227
13.1 History of Immunology 227
13.2 Immunity 228
13.2.1 Innate Immunity 228
13.2.2 Adaptive or Acquired Immunity 229
13.3 The Function of the Immune System - the Example of Tuberculosis 229
13.3.1 The Early Phase of Immune Response: Innate Immune Defense 232
13.3.2 Formation of the Human Tuberculous Granuloma 232
13.3.3 Cell-Mediated Immunity Against M. tuberculosis During Later Phases of Infection 233
13.3.3.1 Cytokine Activation 233
13.3.4 CD4 + T cells 233
13.3.5 CD8 + T cells 234
13.3.6 Unconventional T cells 234
13.3.7 Implications of the Cell-Mediated Immune Response for the Outcome of Tuberculosis and Countermeasures 235
13.3.8 Implications of the Immune Response for Vaccine Development 237
13.3.9 Implications of the Immune Response for Public Health 237
References 238
14 Principles and Practice of Vaccinology 239
14.1 Introduction: Historical Background 239
14.2 Pre-licensing Evaluation of Vaccine 240
14.2.1 Phase I Studies 240
14.2.2 Phase II Studies 241
14.2.3 Phase III Studies 241
14.2.3.1 Vaccine Efficacy (VE) 241
14.3 Programme Implementation 242
14.3.1 Disease Burden in the Pre-vaccination Era 242
14.3.2 Effectiveness and Impact of Intervention 242
14.3.3 Safety of Vaccine (Phase IV Studies) 243
14.3.4 Mathematical Modelling 243
14.3.5 Cost and Cost-Effectiveness of Intervention 243
14.4 Vaccination Strategy 244
14.4.1 Overall Strategy 244
14.4.2 Target Groups 244
14.4.3 Number of Doses 245
14.4.4 Type of Vaccine 245
14.4.5 Delivery Setting 245
14.5 Post-licensing Evaluation 245
14.5.1 Vaccine Coverage 246
14.5.2 Disease Surveillance 246
14.5.3 Outbreak Investigation (Particularly in Highly Vaccinated Populations) 247
14.5.4 Serosurveillance 247
14.5.5 Adverse Event Surveillance 248
14.5.6 Vaccine Effectiveness 249
14.5.7 Acceptability of Intervention 251
14.6 New Vaccines and Methods 252
References 252
15 Health Economics of Infectious Diseases 253
15.1 Introduction 253
15.2 Elements of Economic Evaluation with a Special Focus on Infectious Disease Prevention 254
15.2.1 Effectiveness 254
15.2.2 Comparator and Cost-Effectiveness ratio 258
15.2.3 Perspective 260
15.2.4 Costs 260
15.2.5 Effects 261
15.2.6 Time Horizon 263
15.2.7 Discounting 264
15.2.8 Uncertainty 267
15.2.8.1 Deterministic Sensitivity Analysis 267
15.2.8.2 Probabilistic Sensitivity Analysis (PSA) 268
15.2.9 Transferability 269
15.3 Modeling 270
15.3.1 Common Models for Economic Evaluation 270
15.3.2 Approaches to Consider Indirect Protection Effects 272
15.3.2.1 Static Models 272
15.3.2.2 Dynamic Models 273
15.4 Supporting Decision Making 273
15.5 Conclusions 274
15.6 Looking to the Future 275
References 276
Part III Epidemiology of Particular Infectious Diseases 280
16 Airborne Transmission: Influenza and Tuberculosis 281
16.1 Influenza 281
16.1.1 Pandemic Influenza 282
16.1.2 Pandemic Preparedness Planning 283
16.2 Tuberculosis 284
16.2.1 Current Situation 285
16.2.2 Increase in Tuberculosis Case Numbers 286
16.2.3 Increase of the Rate of Multidrug-Resistant Strains of M. tuberculosis 287
16.2.4 Implementation of the DOTS System in Russia 288
16.2.5 Policy Considerations of WHO 289
16.2.6 Public Health Relevance 290
16.2.6.1 Health System Strengthening 291
References 292
17 Infectious Childhood Diarrhea in Developing Countries 293
17.1 Introduction 293
17.2 Morbidity and Mortality 293
17.2.1 Etiologic Agents 294
17.2.2 Bacterial Agents 294
17.2.3 Viral Agents 297
17.2.4 Protozoa 298
17.3 Risk Factors for Childhood Diarrhea 298
17.3.1 Malnutrition 298
17.3.2 Sanitation and Hygiene 299
17.4 Illness Management 299
17.4.1 Acute Watery Diarrhea 299
17.4.2 Persistent Childhood Diarrhea (PCD) 302
17.4.3 Diagnostic Tests 302
17.4.4 Early Referral 303
17.4.5 Nutritional Therapy and Rehabilitation 303
17.5 Prevention 303
17.5.1 Exclusive Breastfeeding 304
17.5.2 Safe Water 304
17.5.3 Sanitation and Hygiene 305
17.5.4 Vaccines 305
17.5.5 Micronutrients 306
17.6 Conclusion 306
References 307
18 Bloodborne and Sexual Transmission: HIV/AIDS 311
18.1 HIV-1 Pandemic 311
18.1.1 Sub-Saharan Africa 311
18.1.2 Europe and North America 312
18.1.3 Former Soviet Union and Central Asia 312
18.1.4 Southeast Asia 313
18.1.5 Other Areas of the World 313
18.2 HIV Pathogenesis 313
18.2.1 Virology 313
18.2.1.1 HIV-1 313
18.2.1.2 HIV-1 Lifecycle 314
18.2.1.3 HIV-2 315
18.2.2 Immunology 315
18.3 HIV-1 Transmission 316
18.3.1 Sexual Transmission 316
18.3.2 Blood and Blood Products 317
18.3.3 Mother-to-Child Transmission 318
18.4 HIV-1 Disease Progression 319
18.4.1 Natural History 319
18.4.2 Opportunistic Infections and Coinfections 320
18.4.2.1 Tuberculosis 320
18.4.2.2 Hepatitis C Virus 321
18.4.2.3 Hepatitis B Virus 321
18.5 Prevention 321
18.5.1 Behavioral Interventions 322
18.5.2 Prophylactic Antiretroviral Interventions to Prevent MTCT 322
18.5.3 Formula Feeding 323
18.5.4 Caesarean Deliveries 324
18.5.5 Male Circumcision 324
18.5.6 Microbicides 325
18.5.7 HIV-1 Vaccines 325
18.5.8 PEP 326
18.5.9 PREP 327
18.6 Highly Active Antiretroviral Therapy 327
18.6.1 ART Classes 327
18.6.2 HAART 327
18.6.3 Side Effects 328
18.6.4 Adherence 329
18.6.5 Drug Resistance 329
18.6.6 Structured Treatment Interruptions 329
18.6.7 Global Perspectives of HAART 329
18.7 Conclusion 330
References 330
19 Blood Borne and Sexual Transmission: Hepatitis B and C 334
19.1 Introduction 334
19.1.1 Prevalence 335
19.1.2 Prevention 335
19.2 Hepatitis B 336
19.2.1 Epidemiology 336
19.2.1.1 Global Patterns and Transmission Routes 336
19.2.1.2 Risk Groups 336
19.2.2 Molecular Epidemiology 337
19.2.3 Clinical Course 339
19.2.3.1 Diagnostics 339
19.2.3.2 Immunological Reactions 339
19.2.3.3 Clinical Spectrum 341
19.2.3.4 Therapy 342
19.2.4 Prevention and Control 342
19.2.4.1 Hygienic Precautions 342
19.2.4.2 HBV Notification and Post-exposure Prophylaxis 342
19.2.4.3 Universal HBV Vaccination 343
19.2.4.4 Selective Targeted HBV Vaccination 343
19.2.5 Modeling 343
19.3 Hepatitis C 345
19.3.1 Epidemiology of HCV 345
19.3.1.1 Transmission Routes 345
19.3.1.2 Global Pattern 345
19.3.1.3 Risk Groups 345
19.3.2 Virology and Molecular Epidemiology 346
19.3.2.1 Virology 346
19.3.2.2 Molecular Epidemiology 346
19.3.2.3 HCV Superinfection and Reinfection 348
19.3.2.4 Diagnostics 348
19.3.3 Clinical Course of Infection 349
19.3.3.1 Therapy 349
19.3.4 Prevention and Control 350
19.3.4.1 Prevention of Further Spread of HCV 350
19.3.4.2 Identifying Undiagnosed HCV Infections 351
19.3.5 Modeling 352
19.4 Conclusions 352
References 353
20 Sexual Transmission: Chlamydia trachomatis 358
20.1 Introduction 358
20.1.1 Basic Biology 358
20.1.2 Overview of Natural History of C. trachomatis Infection 359
20.2 Descriptive Epidemiology of C. trachomatis Infection 359
20.2.1 Prevalence of C. trachomatis Infection 359
20.2.2 Disease Burden Attributable to C. trachomatis Infection 360
20.2.2.1 Pelvic Inflammatory Disease 360
20.2.2.2 Sequelae of PID 361
20.3 Determinants of the Epidemiology of C. trachomatis Infection 362
20.3.1 Risk of an Initial C. trachomatis Infection 362
20.3.2 Symptoms and Time Course of C. trachomatis Genital Infection 363
20.3.3 Time Course of Complicated C. trachomatis Genital Infection 364
20.3.4 Formation and Dissolution of Sexual Partnerships 365
20.4 Public Health Interventions 366
20.4.1 Dynamic Models of Early Diagnosis and Treatment 366
20.4.2 Cost-Effectiveness of Early Diagnosis and Treatment 368
20.4.3 Public Health Screening and Partner Treatment Programs 369
20.4.3.1 Screening 369
20.4.3.2 Partner Notification 371
20.5 Monitoring Impact of Public Health Interventions 372
20.5.1 Tracking Prevalence of C. trachomatis Infection 372
20.5.2 Tracking Complications and Sequelae 373
20.5.2.1 Pelvic Inflammatory Disease 373
20.5.2.2 Ectopic Pregnancy 374
20.5.2.3 Infertility 374
20.6 Challenges 374
References 375
21 Vector-Borne Transmission: Malaria, Dengue, and Yellow Fever 382
21.1 Malaria 382
21.1.1 The Parasite and Its Life Cycle 383
21.1.2 Course of Disease and Diagnosis 384
21.1.3 Global Distribution and Surveillance 384
21.2 Dengue Fever 386
21.2.1 The Disease and Its Symptoms 387
21.2.2 Pathogenesis: Current Knowledge and Opinions 388
21.2.3 Epidemiology 389
21.3 Yellow Fever 390
References 393
22 Nosocomial Transmission: Methicillin-Resistant S taphylococcus aureus (MRSA) 395
22.1 Introduction 395
22.2 The Burden of Disease 396
22.2.1 Staphylococcus aureus and MRSA 396
22.2.2 Transmission Routes 397
22.2.3 Indirect Transmission of MRSA 397
22.2.4 Intervention Strategies 400
22.3 Mathematical Models for the Dynamics of Hospital-Associated MRSA 401
22.3.1 Insights Derived From Mathematical Models of Hospital-Associated MRSA 402
References 405
23 Infectious Diseases and Cancer: HPV 408
23.1 Introduction 408
23.2 HPV Biology 409
23.2.1 HPV Structure 409
23.2.2 Classification of HPVs and Carcinogenicity 410
23.3 HPV and Human Cancer 411
23.3.1 Cervical Cancer 411
23.3.1.1 Causal Role of HPV in Cervical Cancer 412
23.3.1.2 Natural History of Cervical Cancer 413
23.3.2 Other Anogenital Cancers 414
23.3.2.1 Anal Cancer 415
23.3.2.2 Vaginal Cancer 416
23.3.2.3 Vulvar Cancer 416
23.3.2.4 Penile Cancer 416
23.3.3 Head and Neck Cancer 417
23.3.4 Non-melanoma Skin Cancer 418
23.3.5 Squamous Cell Carcinoma of the Conjunctiva 418
23.4 Other Cancers in Which HPV Is Suspected to Play a Causal Role 419
23.5 Clinical Implications, HPV DNA Testing, and HPV Vaccines 419
23.6 Conclusions 420
References 421
Index 429